Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015071.1 Kokia drynarioides strain JFW-HI SEQ_130115, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42785
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3340 original size:30 final size:30
Alignment explanation
Indices: 3306--3366 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3296 AAATAAAGTT
* **
3306 ACTTTTCGTACTAATAAGTGGTGATAATTG
1 ACTTTTCGTACTAACAAGCAGTGATAATTG
*
3336 ACTTTTCGTATTAACAAGCAGTGATAATTG
1 ACTTTTCGTACTAACAAGCAGTGATAATTG
3366 A
1 A
3367 GGGAGGGGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (30 bp):
ACTTTTCGTACTAACAAGCAGTGATAATTG
Found at i:4165 original size:17 final size:17
Alignment explanation
Indices: 4143--4185 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
4133 TTTAGGGTCT
4143 TTTTGAATGGACGTTTA
1 TTTTGAATGGACGTTTA
4160 TTTTGAATGGACGTTTA
1 TTTTGAATGGACGTTTA
*
4177 TTTTTAATG
1 TTTTGAATG
4186 CAATGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (17 bp):
TTTTGAATGGACGTTTA
Found at i:4503 original size:4 final size:4
Alignment explanation
Indices: 4494--4551 Score: 50
Period size: 4 Copynumber: 15.0 Consensus size: 4
4484 ATCGGTTCGA
* * * *
4494 TAAT TAAT TAAA TAAT TAA- TAAT TAAT AAAAT T-TT TAAT TAAA TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT -TAAT TAAT TAAT TAAT TAAT
4541 TAA- TAAT TAAT
1 TAAT TAAT TAAT
4552 AAAATTTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
3 8 0.19
4 31 0.74
5 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (4 bp):
TAAT
Found at i:4516 original size:7 final size:7
Alignment explanation
Indices: 4498--4553 Score: 58
Period size: 7 Copynumber: 7.4 Consensus size: 7
4488 GTTCGATAAT
4498 TAATTAAA
1 TAATT-AA
4506 TAATTAA
1 TAATTAA
4513 TAATTAA
1 TAATTAA
**
4520 TAAAATTTT
1 T--AATTAA
4529 TAATTAAA
1 TAATT-AA
4537 TAATTAA
1 TAATTAA
4544 TAATTAA
1 TAATTAA
4551 TAA
1 TAA
4554 AATTTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 26 0.63
8 10 0.24
9 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATTAA
Found at i:4526 original size:24 final size:24
Alignment explanation
Indices: 4499--4553 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
4489 TTCGATAATT
4499 AATTAAATAATT-AATAATTAATAA
1 AATT-AATAATTAAATAATTAATAA
**
4523 AATTTTTAATTAAATAATTAAT--
1 AATTAATAATTAAATAATTAATAA
4545 AATTAATAA
1 AATTAATAA
4554 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 7 0.27
23 5 0.19
24 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTAATAATTAAATAATTAATAA
Found at i:4532 original size:31 final size:31
Alignment explanation
Indices: 4497--4559 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4487 GGTTCGATAA
4497 TTAATTAAATAATTAATAATTAATAAAATTT
1 TTAATTAAATAATTAATAATTAATAAAATTT
4528 TTAATTAAATAATTAATAATTAATAAAATTT
1 TTAATTAAATAATTAATAATTAATAAAATTT
4559 T
1 T
4560 AAAAAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTAATTAAATAATTAATAATTAATAAAATTT
Found at i:4580 original size:18 final size:19
Alignment explanation
Indices: 4545--4581 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
4535 AATAATTAAT
4545 AATTAATAAAATTTTAAAA
1 AATTAATAAAATTTTAAAA
4564 AATT-ATAAAATTTTAAAA
1 AATTAATAAAATTTTAAAA
4582 CTGGTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAATAAAATTTTAAAA
Found at i:14160 original size:14 final size:15
Alignment explanation
Indices: 14141--14169 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14131 ATTAGAAAAT
14141 TACTTAATAC-TTAA
1 TACTTAATACATTAA
14155 TACTTAATACATTAA
1 TACTTAATACATTAA
14170 AGTTCACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (15 bp):
TACTTAATACATTAA
Found at i:18778 original size:21 final size:20
Alignment explanation
Indices: 18752--18824 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 20
18742 CAACTCAATC
18752 CTCAATTCTTACTTTTTTATT
1 CTCAATTCTTA-TTTTTTATT
* **
18773 CTCAATTTTTTATTTTCAATT
1 CTCAA-TTCTTATTTTTTATT
* *
18794 GTTAATTCTCTATTTTTTTATT
1 CTCAATTCT-TA-TTTTTTATT
*
18816 CTAAATTCT
1 CTCAATTCT
18825 CAATTTTTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
20 3 0.08
21 17 0.44
22 19 0.49
ACGTcount: A:0.22, C:0.15, G:0.01, T:0.62
Consensus pattern (20 bp):
CTCAATTCTTATTTTTTATT
Found at i:18781 original size:14 final size:14
Alignment explanation
Indices: 18764--18822 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
18754 CAATTCTTAC
18764 TTTTTTATTCTCAA
1 TTTTTTATTCTCAA
*
18778 TTTTTTATTTTCAA
1 TTTTTTATTCTCAA
* * *
18792 TTGTTAATTCTCTAT
1 TTTTTTATTCTC-AA
*
18807 TTTTTTATTCTAAA
1 TTTTTTATTCTCAA
18821 TT
1 TT
18823 CTCAATTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 25 0.71
15 10 0.29
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTTTATTCTCAA
Found at i:18829 original size:29 final size:28
Alignment explanation
Indices: 18770--18829 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
18760 TTACTTTTTT
* * * *
18770 ATTCTCAATTTTTTATTTTCAATTGTTA
1 ATTCTCAATTTTTTATTCTAAATTCTCA
*
18798 ATTCTCTATTTTTTTATTCTAAATTCTCA
1 ATTCTC-AATTTTTTATTCTAAATTCTCA
18827 ATT
1 ATT
18830 TTTTTTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.25, C:0.13, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTCTCAATTTTTTATTCTAAATTCTCA
Found at i:19029 original size:50 final size:50
Alignment explanation
Indices: 18954--19052 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
18944 ATGGTAAGAT
*
18954 AATATCATTAAAATATTTAATTTTAATTAATTAATTATTATGTTGTTAAA
1 AATATCATTAAAATATTAAATTTTAATTAATTAATTATTATGTTGTTAAA
* * * *
19004 AATATTATTAAATTATTAAATTTTAATTAGTTAATTATTATTTTGTTAA
1 AATATCATTAAAATATTAAATTTTAATTAATTAATTATTATGTTGTTAA
19053 CATTTTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (50 bp):
AATATCATTAAAATATTAAATTTTAATTAATTAATTATTATGTTGTTAAA
Found at i:19481 original size:106 final size:105
Alignment explanation
Indices: 19296--19506 Score: 386
Period size: 106 Copynumber: 2.0 Consensus size: 105
19286 GTACAATTAC
* *
19296 ACTAGAGGACGTTAGTTTGCAACTTGGTCTATCGTGTGATGGGGAAGTTGTTACGGGGCCAGTGC
1 ACTAGAAGACGTTAGTTTGCAACTTGGTCTATCGGGTGATGGGGAAGTTGTTACGGGGCCAGTGC
19361 TTAGTGCAAATTGGAGTGCGACATGCGAGCAACTTCTAGG
66 TTAGTGCAAATTGGAGTGCGACATGCGAGCAACTTCTAGG
19401 NACTAGAAGACGTTAGTTTGCAACTTGGTCTATCGGGTGATGGGGAAGTTGTTACGGGGCCAGTG
1 -ACTAGAAGACGTTAGTTTGCAACTTGGTCTATCGGGTGATGGGGAAGTTGTTACGGGGCCAGTG
*
19466 CTTAGTGCAGATTGGAGTGCGACATGCGAGCAACTTCTAGG
65 CTTAGTGCAAATTGGAGTGCGACATGCGAGCAACTTCTAGG
19507 GAAGGTGCCA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27
Consensus pattern (105 bp):
ACTAGAAGACGTTAGTTTGCAACTTGGTCTATCGGGTGATGGGGAAGTTGTTACGGGGCCAGTGC
TTAGTGCAAATTGGAGTGCGACATGCGAGCAACTTCTAGG
Found at i:21702 original size:29 final size:30
Alignment explanation
Indices: 21646--21703 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
21636 TATCAAAATT
*
21646 ATATATGAATTATGGTTTAATGTATAATTGG
1 ATATATGAATTATGATTT-ATGTATAATTGG
* *
21677 ATATATGAATTTTGATTT-TGTGTAATT
1 ATATATGAATTATGATTTATGTATAATT
21704 TTATACATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
31 16 0.67
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (30 bp):
ATATATGAATTATGATTTATGTATAATTGG
Found at i:21898 original size:31 final size:32
Alignment explanation
Indices: 21863--22007 Score: 113
Period size: 31 Copynumber: 4.5 Consensus size: 32
21853 TATATGATTA
21863 AATCAAAATTAAAATTTCA-A-GTATACATTTG
1 AATCAAAATTAAAATTTCACATGTATA-ATTTG
* *
21894 AATCACAATTAGAATTTCACATGTATAA-TTG
1 AATCAAAATTAAAATTTCACATGTATAATTTG
* * *
21925 CATC-AAATTAAAATTCATATATTCAAGTATACATTTG
1 AATCAAAATTAAAATT--T-CA--CATGTATA-ATTTG
* *
21962 AATCACAATTAGAATTTCACATGTATAA-TTG
1 AATCAAAATTAAAATTTCACATGTATAATTTG
*
21993 CATC-AAATTAAAATT
1 AATCAAAATTAAAATT
22008 CATATATTCA
Statistics
Matches: 89, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
30 18 0.20
31 29 0.33
32 4 0.04
33 13 0.15
35 8 0.09
36 2 0.02
37 6 0.07
38 9 0.10
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (32 bp):
AATCAAAATTAAAATTTCACATGTATAATTTG
Found at i:21955 original size:68 final size:68
Alignment explanation
Indices: 21878--22027 Score: 282
Period size: 68 Copynumber: 2.2 Consensus size: 68
21868 AAATTAAAAT
21878 TTCAAGTATACATTTGAATCACAATTAGAATTTCACATGTATAATTGCATCAAATTAAAATTCAT
1 TTCAAGTATACATTTGAATCACAATTAGAATTTCACATGTATAATTGCATCAAATTAAAATTCAT
21943 ATA
66 ATA
21946 TTCAAGTATACATTTGAATCACAATTAGAATTTCACATGTATAATTGCATCAAATTAAAATTCAT
1 TTCAAGTATACATTTGAATCACAATTAGAATTTCACATGTATAATTGCATCAAATTAAAATTCAT
22011 ATA
66 ATA
* *
22014 TTCAATTACACATT
1 TTCAAGTATACATT
22028 AAATCAAAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 80 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (68 bp):
TTCAAGTATACATTTGAATCACAATTAGAATTTCACATGTATAATTGCATCAAATTAAAATTCAT
ATA
Found at i:27585 original size:461 final size:460
Alignment explanation
Indices: 26724--27650 Score: 1667
Period size: 461 Copynumber: 2.0 Consensus size: 460
26714 TCGAGTTGCA
26724 TTAATGCAAAGAACTTAAATATGAACAATTAGAATATTTGAAAGGCCCCATACATGCACGACTAC
1 TTAATGCAAAGAACTTAAATATGAACAATTAGAATATTTGAAAGGCCCCATACATGCACGACTAC
* *
26789 ACGTATGACGTAAGCCATTACAAACTAGATGTGAAAATAATATGCAATTGCATCATGTTATTGGT
66 ACGTATGACGTAAGCCATCACAAACTAGATGTGAAAATAATATGCAATTGCATCATGCTATTGGT
*
26854 AAAATACATGCCTACCATTTTTTGTATTAGGCTTTATTCCCAACATGCAAGCTCGATTCAACTAT
131 AAAATACATGCCTACCATTTTTTGTATTAGGCATTATTCCCAACATGCAAGCTCGATTCAACTAT
*
26919 AAGGTATCTGATAGAAAAGAATGGTGGGCGAAATAGATGGTGATGGTGTAGTTGTATGGTAATAG
196 AAGGTATCTGATAGAAAAGAATGGTGGGCGAAATAGATGGTGATGGAGTAGTTGTATGGTAATAG
*
26984 GGATGCCTCATAAAATAAACTTCGAGGGTGGATAGTCGCGATGCAAGAGTACGCGCTTGATACTG
261 GAATGCCTCATAAAATAAACTTCGAGGGTGGATAGTCGCGATGCAAGAGTACGCGCTTGATACTG
* *
27049 TGGTTGATTTCCAAATATTGCTTTGTAATGGCTCGGAGGATGAACTGTAATTGGGGAGACAAATT
326 TGGTTGATTTCCAAATATTGCTTTGCAATGGCTCGGACGATGAACTGTAATTGGGGAGACAAATT
* * *
27114 TTTCATTGATTGTTTCAGAGGTTTGATCCATGTGGTAGGTTCTTTTCTCATTGTTAGCCATTGAT
391 TTTCATTGATTGTTTAAGACGTTTGATCCATGTGGTAGGGTCTTTTCTCATTGTTAGCCATTGAT
27179 ACAGG
456 ACAGG
* *
27184 TTAATGCAAAGAACTTAAATATGAACAATTAGAATATTTGAGAGGCCCTATACATGCACGACTAC
1 TTAATGCAAAGAACTTAAATATGAACAATTAGAATATTTGAAAGGCCCCATACATGCACGACTAC
27249 ACGTATGACGTAAGACCATCACAAACTAGATGTGAAAATAATATGCAATTGCATCATGCTATTGG
66 ACGTATGACGTAAG-CCATCACAAACTAGATGTGAAAATAATATGCAATTGCATCATGCTATTGG
*
27314 TAAAATACATGCCTACCATTTTTTGTATT-GGTCATTATTGCCAACATGCAAGCTCGATTCAACT
130 TAAAATACATGCCTACCATTTTTTGTATTAGG-CATTATTCCCAACATGCAAGCTCGATTCAACT
27378 ATAAGGTATCTGATAGAAAAGAATGGTGGGCGAAATAGATGGTGATGGAGTAGTTGTATGGTAAT
194 ATAAGGTATCTGATAGAAAAGAATGGTGGGCGAAATAGATGGTGATGGAGTAGTTGTATGGTAAT
* *
27443 AGGAATGCGTCATAAAATAAACTTCGAGGGTGGATAGTCGTGATGCAAGAGTACGCGCTTGATAC
259 AGGAATGCCTCATAAAATAAACTTCGAGGGTGGATAGTCGCGATGCAAGAGTACGCGCTTGATAC
*
27508 TGTGGTTGATTTCCAAATATTGCTTTGCAATGGCTCGGACGATGAGCTGTAATTGGGGAGACAAA
324 TGTGGTTGATTTCCAAATATTGCTTTGCAATGGCTCGGACGATGAACTGTAATTGGGGAGACAAA
**
27573 TTTTTCATTGATTGTTTAAGACGTTTGATCCATGTTTTAGGGTCTTTTCTCATTGTTAGCCATTG
389 TTTTTCATTGATTGTTTAAGACGTTTGATCCATGTGGTAGGGTCTTTTCTCATTGTTAGCCATTG
27638 ATACAGG
454 ATACAGG
27645 TTAATG
1 TTAATG
27651 GTACCTGACT
Statistics
Matches: 447, Mismatches: 18, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
460 79 0.18
461 368 0.82
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (460 bp):
TTAATGCAAAGAACTTAAATATGAACAATTAGAATATTTGAAAGGCCCCATACATGCACGACTAC
ACGTATGACGTAAGCCATCACAAACTAGATGTGAAAATAATATGCAATTGCATCATGCTATTGGT
AAAATACATGCCTACCATTTTTTGTATTAGGCATTATTCCCAACATGCAAGCTCGATTCAACTAT
AAGGTATCTGATAGAAAAGAATGGTGGGCGAAATAGATGGTGATGGAGTAGTTGTATGGTAATAG
GAATGCCTCATAAAATAAACTTCGAGGGTGGATAGTCGCGATGCAAGAGTACGCGCTTGATACTG
TGGTTGATTTCCAAATATTGCTTTGCAATGGCTCGGACGATGAACTGTAATTGGGGAGACAAATT
TTTCATTGATTGTTTAAGACGTTTGATCCATGTGGTAGGGTCTTTTCTCATTGTTAGCCATTGAT
ACAGG
Found at i:34915 original size:302 final size:302
Alignment explanation
Indices: 34369--34978 Score: 1193
Period size: 302 Copynumber: 2.0 Consensus size: 302
34359 TAGCTGGGGA
34369 ATTTGTCCCATAGTTTGTGTGGCCATAATGATAATGAAAGGGTCAATTGACGGGTAATTTGTAAT
1 ATTTGTCCCATAGTTTGTGTGGCCATAATGATAATGAAAGGGTCAATTGACGGGTAATTTGTAAT
*
34434 GTAAAAGACACATTCCCCCAATTTTGTTAATCTTAAGGCCAATGATGTTTTAGCTGTTTGACATT
66 GTAAAAGACAAATTCCCCCAATTTTGTTAATCTTAAGGCCAATGATGTTTTAGCTGTTTGACATT
34499 ATTGCCTTATTCCGATGCTCTTTTATATATAATATGTACATAATTATATAGGTTTGGGGAATAGC
131 ATTGCCTTATTCCGATGCTCTTTTATATATAATATGTACATAATTATATAGGTTTGGGGAATAGC
*
34564 ATCTGTATGTAAAAGCTTTGTGGTTGCCATGCCGCGTATTGCCAGAAGGGTTTGTCCTATCATTT
196 ATCTATATGTAAAAGCTTTGTGGTTGCCATGCCGCGTATTGCCAGAAGGGTTTGTCCTATCATTT
34629 TGTCTCTGTATTTTATCAATCTGTCTGATTTCTTGTTCCAAG
261 TGTCTCTGTATTTTATCAATCTGTCTGATTTCTTGTTCCAAG
34671 ATTTGTCCCATAGTTTGTGTGGCCATAATGATAATGAAAGGGTCAATTGACGGGTAATTTGTAAT
1 ATTTGTCCCATAGTTTGTGTGGCCATAATGATAATGAAAGGGTCAATTGACGGGTAATTTGTAAT
34736 GTAAAAGACAAATTCCCCCAATTTTGTTAATCTTAAGGCCAATGATGTTTTAGCTGTTTGACATT
66 GTAAAAGACAAATTCCCCCAATTTTGTTAATCTTAAGGCCAATGATGTTTTAGCTGTTTGACATT
*
34801 ATTGCCTTATTCTGATGCTCTTTTATATATAATATGTACATAATTATATAGGTTTGGGGAATAGC
131 ATTGCCTTATTCCGATGCTCTTTTATATATAATATGTACATAATTATATAGGTTTGGGGAATAGC
34866 ATCTATATGTAAAAGCTTTGTGGTTGCCATGCCGCGTATTGCCAGAAGGGTTTGTCCTATCATTT
196 ATCTATATGTAAAAGCTTTGTGGTTGCCATGCCGCGTATTGCCAGAAGGGTTTGTCCTATCATTT
34931 TGTCTCTGTATTTTATCAATCTGTCTGATTTCTTGTTCCAAG
261 TGTCTCTGTATTTTATCAATCTGTCTGATTTCTTGTTCCAAG
34973 ATTTGT
1 ATTTGT
34979 GTTCGAATCT
Statistics
Matches: 305, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
302 305 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (302 bp):
ATTTGTCCCATAGTTTGTGTGGCCATAATGATAATGAAAGGGTCAATTGACGGGTAATTTGTAAT
GTAAAAGACAAATTCCCCCAATTTTGTTAATCTTAAGGCCAATGATGTTTTAGCTGTTTGACATT
ATTGCCTTATTCCGATGCTCTTTTATATATAATATGTACATAATTATATAGGTTTGGGGAATAGC
ATCTATATGTAAAAGCTTTGTGGTTGCCATGCCGCGTATTGCCAGAAGGGTTTGTCCTATCATTT
TGTCTCTGTATTTTATCAATCTGTCTGATTTCTTGTTCCAAG
Found at i:37407 original size:14 final size:15
Alignment explanation
Indices: 37373--37414 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
37363 TAAATTAGAT
37373 TATATAAATATATTA
1 TATATAAATATATTA
* *
37388 TTTATAAA-ATTTTA
1 TATATAAATATATTA
37402 TATATATAATATA
1 TATATA-AATATA
37415 AAATTAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 10 0.48
15 9 0.43
16 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATAAATATATTA
Found at i:38030 original size:28 final size:29
Alignment explanation
Indices: 37998--38054 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
37988 TATTTAAGTT
*
37998 TTTTTTTTTCT-CTAATTTGATACCTAAA
1 TTTTTTTTTCTCCGAATTTGATACCTAAA
* *
38026 TTTTTTTTTGTCCGATTTTGATACCTAAA
1 TTTTTTTTTCTCCGAATTTGATACCTAAA
38055 CTCGTCAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTTTTTTTCTCCGAATTTGATACCTAAA
Found at i:42075 original size:15 final size:15
Alignment explanation
Indices: 42025--42082 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
42015 ATTTAATTAT
42025 TTAATTTTGAT-TTATA
1 TTAATTTT-ATATT-TA
*
42041 TTAATTTAATATTTA
1 TTAATTTTATATTTA
* *
42056 ATAATTTTATATTTT
1 TTAATTTTATATTTA
42071 TTAATTTTATAT
1 TTAATTTTATAT
42083 AGAGTCATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 27 0.75
16 9 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTAATTTTATATTTA
Done.